Multiple sequence alignment - TraesCS5D01G342900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)



BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G342900 chr5D 100.000 2423 0 0 1 2423 431126274 431128696 0.000000e+00 4475.0
1 TraesCS5D01G342900 chr5D 92.208 154 7 2 1823 1976 29486605 29486457 1.890000e-51 213.0
2 TraesCS5D01G342900 chr5D 95.745 47 1 1 1650 1696 98437169 98437214 9.290000e-10 75.0
3 TraesCS5D01G342900 chr5D 81.818 88 12 4 707 791 339070994 339071080 1.200000e-08 71.3
4 TraesCS5D01G342900 chr5D 87.273 55 5 1 1651 1705 141214664 141214612 7.230000e-06 62.1
5 TraesCS5D01G342900 chr5D 97.222 36 0 1 708 742 414770747 414770712 2.600000e-05 60.2
6 TraesCS5D01G342900 chr5B 91.133 1703 99 20 171 1828 520551089 520552784 0.000000e+00 2261.0
7 TraesCS5D01G342900 chr5B 93.548 186 11 1 1 186 520550512 520550696 2.370000e-70 276.0
8 TraesCS5D01G342900 chr5B 90.452 199 18 1 2225 2422 520553505 520553703 6.640000e-66 261.0
9 TraesCS5D01G342900 chr5A 86.634 1025 86 28 659 1653 546385269 546386272 0.000000e+00 1086.0
10 TraesCS5D01G342900 chr5A 89.168 517 29 11 157 661 546384722 546385223 9.520000e-174 619.0
11 TraesCS5D01G342900 chr5A 96.241 133 5 0 411 543 504869441 504869573 4.060000e-53 219.0
12 TraesCS5D01G342900 chr5A 87.755 49 5 1 708 755 546343308 546343260 3.370000e-04 56.5
13 TraesCS5D01G342900 chrUn 92.157 153 10 2 1825 1976 334937675 334937524 5.250000e-52 215.0
14 TraesCS5D01G342900 chr3B 90.798 163 11 4 1816 1976 57244712 57244872 5.250000e-52 215.0
15 TraesCS5D01G342900 chr3B 90.798 163 11 4 1816 1976 57272134 57272294 5.250000e-52 215.0
16 TraesCS5D01G342900 chr3B 93.617 47 1 1 1650 1696 431771259 431771303 4.320000e-08 69.4
17 TraesCS5D01G342900 chr1D 92.414 145 9 2 1825 1968 269813369 269813226 3.160000e-49 206.0
18 TraesCS5D01G342900 chr1D 90.066 151 11 4 1825 1974 124675032 124674885 2.460000e-45 193.0
19 TraesCS5D01G342900 chr7D 90.000 160 9 5 1816 1974 530411025 530411178 1.470000e-47 200.0
20 TraesCS5D01G342900 chr7D 84.404 109 13 4 2255 2360 629242510 629242403 1.180000e-18 104.0
21 TraesCS5D01G342900 chr6D 90.789 152 11 3 1825 1976 329884380 329884232 1.470000e-47 200.0
22 TraesCS5D01G342900 chr6D 100.000 28 0 0 2129 2156 467150607 467150634 4.000000e-03 52.8
23 TraesCS5D01G342900 chr4A 89.474 152 12 4 1825 1974 433665489 433665340 3.180000e-44 189.0
24 TraesCS5D01G342900 chr3D 95.652 46 1 1 1651 1696 450346595 450346639 3.340000e-09 73.1
25 TraesCS5D01G342900 chr1A 84.416 77 9 3 717 791 573386371 573386446 3.340000e-09 73.1
26 TraesCS5D01G342900 chr6A 83.333 84 6 7 717 797 103672844 103672766 1.200000e-08 71.3
27 TraesCS5D01G342900 chr1B 81.818 88 12 4 707 791 395203829 395203743 1.200000e-08 71.3
28 TraesCS5D01G342900 chr6B 93.617 47 1 1 1647 1693 39949606 39949650 4.320000e-08 69.4
29 TraesCS5D01G342900 chr2B 93.617 47 1 1 1650 1696 457550629 457550585 4.320000e-08 69.4
30 TraesCS5D01G342900 chr7A 83.117 77 10 3 717 791 664772675 664772600 1.550000e-07 67.6
31 TraesCS5D01G342900 chr4D 93.478 46 1 1 1648 1693 54763618 54763661 1.550000e-07 67.6
32 TraesCS5D01G342900 chr7B 87.500 56 5 1 1650 1705 613317926 613317873 2.010000e-06 63.9
33 TraesCS5D01G342900 chr4B 96.970 33 0 1 2126 2157 387798866 387798834 1.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G342900 chr5D 431126274 431128696 2422 False 4475.000000 4475 100.000 1 2423 1 chr5D.!!$F3 2422
1 TraesCS5D01G342900 chr5B 520550512 520553703 3191 False 932.666667 2261 91.711 1 2422 3 chr5B.!!$F1 2421
2 TraesCS5D01G342900 chr5A 546384722 546386272 1550 False 852.500000 1086 87.901 157 1653 2 chr5A.!!$F2 1496


AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
64 65 0.370273 CTTCGGAGTTTGATTCGCCG 59.63 55.0 0.0 0.0 46.42 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2057 2717 0.182775 AGGCTCACGGGTGAAAAACT 59.817 50.0 2.81 0.0 39.39 2.66 R


All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 5.469084 GGGATTAATTAGTTTAGGGTGCGAG 59.531 44.000 0.00 0.00 0.00 5.03
48 49 3.364366 CGAGTGACAGGCATTTTGACTTC 60.364 47.826 0.00 0.00 29.42 3.01
49 50 2.549754 AGTGACAGGCATTTTGACTTCG 59.450 45.455 0.00 0.00 29.42 3.79
51 52 2.151202 GACAGGCATTTTGACTTCGGA 58.849 47.619 0.00 0.00 29.42 4.55
64 65 0.370273 CTTCGGAGTTTGATTCGCCG 59.630 55.000 0.00 0.00 46.42 6.46
239 652 1.598132 GACGATTCTGTCTCGATCGGA 59.402 52.381 16.41 8.74 39.38 4.55
288 701 3.636043 ACAAAGTGGACGCACGCG 61.636 61.111 10.36 10.36 46.03 6.01
291 704 2.380410 AAAGTGGACGCACGCGATC 61.380 57.895 19.66 11.41 42.83 3.69
313 726 4.133078 CAATTCCAACTGCCTATCTCTCC 58.867 47.826 0.00 0.00 0.00 3.71
475 918 1.213094 ACGACGCGGAACAAAGACTG 61.213 55.000 12.47 0.00 0.00 3.51
685 1177 6.617371 AGATATGTACATTTGTCCTTCCTCCT 59.383 38.462 14.77 0.00 0.00 3.69
688 1180 5.701224 TGTACATTTGTCCTTCCTCCTTTT 58.299 37.500 0.00 0.00 0.00 2.27
779 1271 8.854979 TTCATTCATGCAATAAGTAATTTCGG 57.145 30.769 0.00 0.00 0.00 4.30
785 1280 4.569162 TGCAATAAGTAATTTCGGACGGAG 59.431 41.667 0.00 0.00 0.00 4.63
786 1281 4.025145 GCAATAAGTAATTTCGGACGGAGG 60.025 45.833 0.00 0.00 0.00 4.30
787 1282 2.685850 AAGTAATTTCGGACGGAGGG 57.314 50.000 0.00 0.00 0.00 4.30
799 1294 2.228925 GACGGAGGGGTAGTAGATGAC 58.771 57.143 0.00 0.00 0.00 3.06
883 1381 5.079689 TCTGTTGACGCCATGAATAACTA 57.920 39.130 0.00 0.00 0.00 2.24
884 1382 5.670485 TCTGTTGACGCCATGAATAACTAT 58.330 37.500 0.00 0.00 0.00 2.12
918 1416 7.009907 GCTTTTTCTGACATTTTATCATGCTCC 59.990 37.037 0.00 0.00 0.00 4.70
938 1436 2.422803 CCAGAGAACCAAAACAGTCCCA 60.423 50.000 0.00 0.00 0.00 4.37
962 1460 0.788391 GGTCATTCGGTCAACACGAC 59.212 55.000 0.00 0.00 44.57 4.34
1030 1529 1.666599 CCAATTGTCACCGTACGTCGA 60.667 52.381 15.21 7.15 42.86 4.20
1035 1534 4.388080 CACCGTACGTCGACCGCA 62.388 66.667 15.21 0.00 42.86 5.69
1093 1592 0.604511 CCTACAAAAACCCGGCGACT 60.605 55.000 9.30 0.00 0.00 4.18
1460 1983 2.672307 TGCATGGCATCGCACACA 60.672 55.556 16.90 0.00 31.71 3.72
1474 1997 1.798223 GCACACAACTCAAGATACGCA 59.202 47.619 0.00 0.00 0.00 5.24
1481 2004 1.733912 ACTCAAGATACGCACGTACGA 59.266 47.619 24.41 0.00 36.70 3.43
1505 2029 1.089481 TCATCGGAGGAAACATGCGC 61.089 55.000 0.00 0.00 0.00 6.09
1552 2082 4.090034 CGTTCGTGACTAGCTAGTTCTTC 58.910 47.826 26.71 14.64 36.50 2.87
1568 2098 8.454106 GCTAGTTCTTCTTGAATTCATTTGCTA 58.546 33.333 9.40 5.46 36.99 3.49
1684 2214 7.389053 AGTTCTTGATTGTTTTTCGAGATAGCT 59.611 33.333 0.00 0.00 34.39 3.32
1713 2243 6.291743 CGCTTATTTCACGCGGTAAGTTTATA 60.292 38.462 12.47 0.00 42.88 0.98
1780 2310 3.307108 TGTGGGTGCCGATCGTCA 61.307 61.111 15.09 4.04 0.00 4.35
1785 2315 0.946221 GGGTGCCGATCGTCATCATC 60.946 60.000 11.95 5.34 0.00 2.92
1823 2353 8.589701 TTTTCGCTGTATCTCCTATATATGGA 57.410 34.615 0.00 1.27 0.00 3.41
1824 2354 7.569639 TTCGCTGTATCTCCTATATATGGAC 57.430 40.000 0.00 0.00 0.00 4.02
1825 2355 6.659824 TCGCTGTATCTCCTATATATGGACA 58.340 40.000 0.00 0.00 0.00 4.02
1827 2357 7.283354 TCGCTGTATCTCCTATATATGGACAAG 59.717 40.741 0.00 0.00 0.00 3.16
1828 2358 7.283354 CGCTGTATCTCCTATATATGGACAAGA 59.717 40.741 0.00 0.00 0.00 3.02
1829 2359 9.142014 GCTGTATCTCCTATATATGGACAAGAT 57.858 37.037 0.00 5.93 0.00 2.40
1834 2364 8.815565 TCTCCTATATATGGACAAGATGAGTC 57.184 38.462 0.00 0.00 35.29 3.36
1835 2365 8.619281 TCTCCTATATATGGACAAGATGAGTCT 58.381 37.037 0.00 0.00 36.29 3.24
1841 2371 5.736951 ATGGACAAGATGAGTCTATAGCC 57.263 43.478 0.00 0.00 35.74 3.93
1842 2372 4.809193 TGGACAAGATGAGTCTATAGCCT 58.191 43.478 0.00 0.00 36.29 4.58
1843 2373 5.953571 TGGACAAGATGAGTCTATAGCCTA 58.046 41.667 0.00 0.00 36.29 3.93
1844 2374 6.373759 TGGACAAGATGAGTCTATAGCCTAA 58.626 40.000 0.00 0.00 36.29 2.69
1845 2375 7.013220 TGGACAAGATGAGTCTATAGCCTAAT 58.987 38.462 0.00 0.00 36.29 1.73
1846 2376 8.170730 TGGACAAGATGAGTCTATAGCCTAATA 58.829 37.037 0.00 0.00 36.29 0.98
1863 2393 8.807948 AGCCTAATAAATGAAGTGTTACATGT 57.192 30.769 2.69 2.69 0.00 3.21
1864 2394 9.243105 AGCCTAATAAATGAAGTGTTACATGTT 57.757 29.630 2.30 0.00 0.00 2.71
1871 2401 5.994887 TGAAGTGTTACATGTTACCACAC 57.005 39.130 12.16 14.80 38.43 3.82
1872 2402 5.429130 TGAAGTGTTACATGTTACCACACA 58.571 37.500 22.19 17.31 40.23 3.72
1876 2406 7.609760 AGTGTTACATGTTACCACACATATG 57.390 36.000 22.19 0.00 40.23 1.78
1878 2408 7.663905 AGTGTTACATGTTACCACACATATGTT 59.336 33.333 22.19 0.00 40.23 2.71
1879 2409 8.937884 GTGTTACATGTTACCACACATATGTTA 58.062 33.333 12.16 0.00 36.72 2.41
1880 2410 8.937884 TGTTACATGTTACCACACATATGTTAC 58.062 33.333 12.16 0.00 36.72 2.50
1882 2412 7.843490 ACATGTTACCACACATATGTTACTC 57.157 36.000 5.37 0.00 36.72 2.59
1883 2413 6.821665 ACATGTTACCACACATATGTTACTCC 59.178 38.462 5.37 0.00 36.72 3.85
1885 2415 3.926058 ACCACACATATGTTACTCCCC 57.074 47.619 5.37 0.00 36.72 4.81
1886 2416 3.186283 ACCACACATATGTTACTCCCCA 58.814 45.455 5.37 0.00 36.72 4.96
1887 2417 3.054655 ACCACACATATGTTACTCCCCAC 60.055 47.826 5.37 0.00 36.72 4.61
1888 2418 3.199946 CCACACATATGTTACTCCCCACT 59.800 47.826 5.37 0.00 36.72 4.00
1889 2419 4.407621 CCACACATATGTTACTCCCCACTA 59.592 45.833 5.37 0.00 36.72 2.74
1890 2420 5.071788 CCACACATATGTTACTCCCCACTAT 59.928 44.000 5.37 0.00 36.72 2.12
1891 2421 6.269077 CCACACATATGTTACTCCCCACTATA 59.731 42.308 5.37 0.00 36.72 1.31
1892 2422 7.378966 CACACATATGTTACTCCCCACTATAG 58.621 42.308 5.37 0.00 36.72 1.31
1893 2423 7.232737 CACACATATGTTACTCCCCACTATAGA 59.767 40.741 5.37 0.00 36.72 1.98
1895 2425 6.954684 ACATATGTTACTCCCCACTATAGAGG 59.045 42.308 6.78 8.10 31.70 3.69
1896 2426 4.894252 TGTTACTCCCCACTATAGAGGT 57.106 45.455 14.29 0.00 31.70 3.85
1897 2427 5.999987 TGTTACTCCCCACTATAGAGGTA 57.000 43.478 14.29 2.62 31.70 3.08
1898 2428 5.950023 TGTTACTCCCCACTATAGAGGTAG 58.050 45.833 14.29 12.87 31.70 3.18
1900 2430 6.621098 TGTTACTCCCCACTATAGAGGTAGTA 59.379 42.308 17.42 17.42 33.29 1.82
1901 2431 7.129349 TGTTACTCCCCACTATAGAGGTAGTAA 59.871 40.741 23.15 23.15 33.91 2.24
1902 2432 5.951204 ACTCCCCACTATAGAGGTAGTAAC 58.049 45.833 14.29 0.00 33.29 2.50
1904 2434 6.104392 ACTCCCCACTATAGAGGTAGTAACAT 59.896 42.308 14.29 0.00 33.29 2.71
1905 2435 7.296628 ACTCCCCACTATAGAGGTAGTAACATA 59.703 40.741 14.29 0.00 33.29 2.29
1906 2436 7.696981 TCCCCACTATAGAGGTAGTAACATAG 58.303 42.308 14.29 0.00 33.29 2.23
1907 2437 7.518653 TCCCCACTATAGAGGTAGTAACATAGA 59.481 40.741 14.29 0.00 33.29 1.98
1908 2438 7.830201 CCCCACTATAGAGGTAGTAACATAGAG 59.170 44.444 14.29 0.00 33.29 2.43
1919 2449 9.917887 AGGTAGTAACATAGAGTAGTAACATGT 57.082 33.333 0.00 0.00 0.00 3.21
1978 2638 5.810080 ACCCATTATGGCTAGTCTTACTC 57.190 43.478 5.57 0.00 35.79 2.59
2005 2665 6.650807 CACACAATGTCTACTTTAGTGTGGAT 59.349 38.462 20.92 0.41 46.82 3.41
2006 2666 6.874134 ACACAATGTCTACTTTAGTGTGGATC 59.126 38.462 8.56 0.00 37.35 3.36
2034 2694 3.731547 TGGCCTGACCAGATGGAG 58.268 61.111 3.32 0.00 46.36 3.86
2035 2695 1.997311 TGGCCTGACCAGATGGAGG 60.997 63.158 3.32 4.04 46.36 4.30
2036 2696 2.191641 GCCTGACCAGATGGAGGC 59.808 66.667 14.00 14.00 44.63 4.70
2039 2699 0.107312 CCTGACCAGATGGAGGCTTG 60.107 60.000 5.72 0.00 38.94 4.01
2065 2725 1.412343 GGCTTTGGCTCCAGTTTTTCA 59.588 47.619 0.00 0.00 38.73 2.69
2066 2726 2.473816 GCTTTGGCTCCAGTTTTTCAC 58.526 47.619 0.00 0.00 35.22 3.18
2074 2734 0.310854 CCAGTTTTTCACCCGTGAGC 59.689 55.000 0.00 0.00 41.13 4.26
2103 2763 5.393124 CCGAAAACCCGAATACTTAAAACC 58.607 41.667 0.00 0.00 0.00 3.27
2127 2787 5.981088 ATGACTTGGTGAAAATATGTGCA 57.019 34.783 0.00 0.00 0.00 4.57
2139 2799 0.179048 TATGTGCATTGCTCCCTCCG 60.179 55.000 10.49 0.00 0.00 4.63
2154 2814 3.581332 TCCCTCCGTCTCAAAATAAGTGT 59.419 43.478 0.00 0.00 0.00 3.55
2236 3099 9.823647 CCTATAACTTCATTCATACTCACAACT 57.176 33.333 0.00 0.00 0.00 3.16
2278 3141 7.945033 TTTGAACCATGCTTCAAGAAATTAC 57.055 32.000 14.24 0.00 40.42 1.89
2298 3161 7.907214 ATTACAAACAACTCCTACAGCTAAG 57.093 36.000 0.00 0.00 0.00 2.18
2328 3192 6.894103 ACAATAAATCTCTTGGAGGCATCTTT 59.106 34.615 0.00 0.00 0.00 2.52
2334 3198 2.569853 TCTTGGAGGCATCTTTTCCGTA 59.430 45.455 0.00 0.00 33.60 4.02
2343 3207 4.272748 GGCATCTTTTCCGTAGTATCAACC 59.727 45.833 0.00 0.00 0.00 3.77
2354 3218 5.220662 CCGTAGTATCAACCTTTGCAAGATG 60.221 44.000 0.00 0.00 0.00 2.90
2359 3223 8.579850 AGTATCAACCTTTGCAAGATGAAATA 57.420 30.769 0.00 0.00 31.25 1.40
2372 3236 7.982371 CAAGATGAAATATTGCCAAGACTTC 57.018 36.000 0.00 0.00 38.83 3.01
2385 3249 4.378459 GCCAAGACTTCAACAAATAGACCG 60.378 45.833 0.00 0.00 0.00 4.79
2388 3252 4.385825 AGACTTCAACAAATAGACCGCAA 58.614 39.130 0.00 0.00 0.00 4.85
2391 3255 5.699839 ACTTCAACAAATAGACCGCAATTC 58.300 37.500 0.00 0.00 0.00 2.17
2397 3261 2.225068 ATAGACCGCAATTCGACTGG 57.775 50.000 0.00 0.00 41.67 4.00
2412 3276 0.663688 ACTGGAGTAGCGATACTGCG 59.336 55.000 24.20 20.41 40.66 5.18
2422 3286 1.457738 CGATACTGCGACTCGTTCAG 58.542 55.000 0.00 2.68 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.212636 CGCACCCTAAACTAATTAATCCCG 59.787 45.833 0.00 0.00 0.00 5.14
11 12 4.251268 GTCACTCGCACCCTAAACTAATT 58.749 43.478 0.00 0.00 0.00 1.40
29 30 2.350772 CCGAAGTCAAAATGCCTGTCAC 60.351 50.000 0.00 0.00 0.00 3.67
48 49 0.736325 ACTCGGCGAATCAAACTCCG 60.736 55.000 12.13 0.00 41.30 4.63
49 50 0.721718 CACTCGGCGAATCAAACTCC 59.278 55.000 12.13 0.00 0.00 3.85
51 52 2.162716 GCACTCGGCGAATCAAACT 58.837 52.632 12.13 0.00 0.00 2.66
64 65 3.503363 GCATCGCCACCTGCACTC 61.503 66.667 0.00 0.00 41.33 3.51
239 652 1.517832 CGAAATCGCCTCACCCTCT 59.482 57.895 0.00 0.00 0.00 3.69
288 701 5.619220 AGAGATAGGCAGTTGGAATTGATC 58.381 41.667 0.00 0.00 0.00 2.92
291 704 4.133078 GGAGAGATAGGCAGTTGGAATTG 58.867 47.826 0.00 0.00 0.00 2.32
313 726 3.875838 TTTTTGACCAAATCGCGGG 57.124 47.368 6.13 0.89 0.00 6.13
419 841 2.612567 TTGGGCGACGACAATGTGC 61.613 57.895 1.63 0.00 0.00 4.57
420 842 1.206578 GTTGGGCGACGACAATGTG 59.793 57.895 1.63 0.00 33.39 3.21
421 843 1.227704 TGTTGGGCGACGACAATGT 60.228 52.632 1.63 0.00 40.53 2.71
475 918 2.484889 GGTGAGCTCCCGAATTATGTC 58.515 52.381 12.15 0.00 0.00 3.06
593 1036 6.287589 AGAGTAACCGATTCAAGAGTTGAT 57.712 37.500 0.00 0.00 39.84 2.57
669 1161 5.789643 TCAAAAAGGAGGAAGGACAAATG 57.210 39.130 0.00 0.00 0.00 2.32
676 1168 9.243105 TGATAAGTAATTCAAAAAGGAGGAAGG 57.757 33.333 0.00 0.00 0.00 3.46
760 1252 5.007234 TCCGTCCGAAATTACTTATTGCATG 59.993 40.000 0.00 0.00 0.00 4.06
779 1271 2.158638 AGTCATCTACTACCCCTCCGTC 60.159 54.545 0.00 0.00 36.36 4.79
785 1280 4.820894 AACAACAGTCATCTACTACCCC 57.179 45.455 0.00 0.00 35.76 4.95
786 1281 5.790593 TGAAACAACAGTCATCTACTACCC 58.209 41.667 0.00 0.00 35.76 3.69
787 1282 6.688578 TCTGAAACAACAGTCATCTACTACC 58.311 40.000 0.00 0.00 35.76 3.18
799 1294 6.549912 TGACATGAAGATCTGAAACAACAG 57.450 37.500 0.00 0.00 39.02 3.16
883 1381 8.424274 AAAATGTCAGAAAAAGCGAGAAAAAT 57.576 26.923 0.00 0.00 0.00 1.82
884 1382 7.826260 AAAATGTCAGAAAAAGCGAGAAAAA 57.174 28.000 0.00 0.00 0.00 1.94
918 1416 2.618709 GTGGGACTGTTTTGGTTCTCTG 59.381 50.000 0.00 0.00 0.00 3.35
962 1460 1.012486 GCGTTACCACTGTTCCTCGG 61.012 60.000 0.00 0.00 0.00 4.63
1030 1529 2.042831 GCCATGAGAGCTTTGCGGT 61.043 57.895 0.00 0.00 0.00 5.68
1035 1534 2.439156 GGCGGCCATGAGAGCTTT 60.439 61.111 15.62 0.00 0.00 3.51
1096 1595 2.750888 GCGATGCTTGGACGGGAAC 61.751 63.158 0.00 0.00 0.00 3.62
1414 1930 2.590007 ATGATCGGCTCAAGCGGC 60.590 61.111 4.80 0.00 43.26 6.53
1460 1983 2.160219 TCGTACGTGCGTATCTTGAGTT 59.840 45.455 24.94 0.00 32.82 3.01
1505 2029 2.789917 GAACAGAGCATGCAGGCG 59.210 61.111 21.98 6.43 39.27 5.52
1515 2039 2.724690 ACGAACGAATGAACGAACAGAG 59.275 45.455 0.14 0.00 37.03 3.35
1516 2040 2.469886 CACGAACGAATGAACGAACAGA 59.530 45.455 0.14 0.00 37.03 3.41
1552 2082 9.414295 TCAAAGACAATAGCAAATGAATTCAAG 57.586 29.630 13.09 6.87 0.00 3.02
1568 2098 6.282930 CACCAGGTTGAAAATCAAAGACAAT 58.717 36.000 0.00 0.00 38.22 2.71
1582 2112 2.186160 CAAGCACGCACCAGGTTGA 61.186 57.895 0.00 0.00 43.77 3.18
1655 2185 5.751509 TCTCGAAAAACAATCAAGAACTCGA 59.248 36.000 0.00 0.00 0.00 4.04
1665 2195 5.050972 CGGGTAGCTATCTCGAAAAACAATC 60.051 44.000 3.53 0.00 0.00 2.67
1666 2196 4.809426 CGGGTAGCTATCTCGAAAAACAAT 59.191 41.667 3.53 0.00 0.00 2.71
1780 2310 9.941664 CAGCGAAAATAATTAACAAGAGATGAT 57.058 29.630 0.00 0.00 0.00 2.45
1801 2331 6.659824 TGTCCATATATAGGAGATACAGCGA 58.340 40.000 0.00 0.00 35.42 4.93
1815 2345 9.142014 GGCTATAGACTCATCTTGTCCATATAT 57.858 37.037 3.21 0.00 36.29 0.86
1819 2349 5.401750 AGGCTATAGACTCATCTTGTCCAT 58.598 41.667 0.83 0.00 36.29 3.41
1821 2351 6.902771 TTAGGCTATAGACTCATCTTGTCC 57.097 41.667 12.64 0.00 36.29 4.02
1862 2392 5.121105 GGGGAGTAACATATGTGTGGTAAC 58.879 45.833 9.63 1.91 38.92 2.50
1863 2393 4.783763 TGGGGAGTAACATATGTGTGGTAA 59.216 41.667 9.63 0.00 38.92 2.85
1864 2394 4.162698 GTGGGGAGTAACATATGTGTGGTA 59.837 45.833 9.63 0.00 38.92 3.25
1866 2396 3.199946 AGTGGGGAGTAACATATGTGTGG 59.800 47.826 9.63 0.00 38.92 4.17
1867 2397 4.487714 AGTGGGGAGTAACATATGTGTG 57.512 45.455 9.63 0.00 38.92 3.82
1869 2399 7.093727 CCTCTATAGTGGGGAGTAACATATGTG 60.094 44.444 9.63 0.00 0.00 3.21
1871 2401 6.954684 ACCTCTATAGTGGGGAGTAACATATG 59.045 42.308 21.82 0.00 33.22 1.78
1872 2402 7.117331 ACCTCTATAGTGGGGAGTAACATAT 57.883 40.000 21.82 0.00 33.22 1.78
1876 2406 5.951204 ACTACCTCTATAGTGGGGAGTAAC 58.049 45.833 22.09 0.00 34.02 2.50
1878 2408 6.621098 TGTTACTACCTCTATAGTGGGGAGTA 59.379 42.308 23.32 23.32 36.09 2.59
1879 2409 5.434376 TGTTACTACCTCTATAGTGGGGAGT 59.566 44.000 24.72 24.72 36.09 3.85
1880 2410 5.950023 TGTTACTACCTCTATAGTGGGGAG 58.050 45.833 21.82 20.04 36.09 4.30
1882 2412 7.696981 TCTATGTTACTACCTCTATAGTGGGG 58.303 42.308 21.82 16.35 36.09 4.96
1883 2413 8.384718 ACTCTATGTTACTACCTCTATAGTGGG 58.615 40.741 21.82 16.23 36.09 4.61
1893 2423 9.917887 ACATGTTACTACTCTATGTTACTACCT 57.082 33.333 0.00 0.00 0.00 3.08
1957 2487 5.540337 TGAGAGTAAGACTAGCCATAATGGG 59.460 44.000 0.00 0.00 38.19 4.00
1958 2488 6.040955 TGTGAGAGTAAGACTAGCCATAATGG 59.959 42.308 0.00 0.00 41.55 3.16
1959 2489 6.920758 GTGTGAGAGTAAGACTAGCCATAATG 59.079 42.308 0.00 0.00 0.00 1.90
1961 2491 5.949952 TGTGTGAGAGTAAGACTAGCCATAA 59.050 40.000 0.00 0.00 0.00 1.90
1963 2493 4.344978 TGTGTGAGAGTAAGACTAGCCAT 58.655 43.478 0.00 0.00 0.00 4.40
1966 2496 5.715070 ACATTGTGTGAGAGTAAGACTAGC 58.285 41.667 0.00 0.00 0.00 3.42
1967 2497 7.151999 AGACATTGTGTGAGAGTAAGACTAG 57.848 40.000 0.00 0.00 0.00 2.57
1969 2499 6.717540 AGTAGACATTGTGTGAGAGTAAGACT 59.282 38.462 0.00 0.00 0.00 3.24
1970 2500 6.915349 AGTAGACATTGTGTGAGAGTAAGAC 58.085 40.000 0.00 0.00 0.00 3.01
1971 2501 7.526142 AAGTAGACATTGTGTGAGAGTAAGA 57.474 36.000 0.00 0.00 0.00 2.10
2029 2689 3.801997 CCCGCTCCAAGCCTCCAT 61.802 66.667 0.00 0.00 38.18 3.41
2032 2692 3.927481 AAAGCCCGCTCCAAGCCTC 62.927 63.158 0.00 0.00 38.18 4.70
2033 2693 3.971702 AAAGCCCGCTCCAAGCCT 61.972 61.111 0.00 0.00 38.18 4.58
2034 2694 3.752339 CAAAGCCCGCTCCAAGCC 61.752 66.667 0.00 0.00 38.18 4.35
2035 2695 3.752339 CCAAAGCCCGCTCCAAGC 61.752 66.667 0.00 0.00 38.02 4.01
2036 2696 3.752339 GCCAAAGCCCGCTCCAAG 61.752 66.667 0.00 0.00 0.00 3.61
2057 2717 0.182775 AGGCTCACGGGTGAAAAACT 59.817 50.000 2.81 0.00 39.39 2.66
2074 2734 3.733295 TATTCGGGTTTTCGGCCCAGG 62.733 57.143 0.00 0.00 46.40 4.45
2089 2749 8.388103 CACCAAGTCATAGGTTTTAAGTATTCG 58.612 37.037 0.00 0.00 35.52 3.34
2090 2750 9.444600 TCACCAAGTCATAGGTTTTAAGTATTC 57.555 33.333 0.00 0.00 35.52 1.75
2103 2763 7.087409 TGCACATATTTTCACCAAGTCATAG 57.913 36.000 0.00 0.00 0.00 2.23
2123 2783 2.045926 ACGGAGGGAGCAATGCAC 60.046 61.111 8.35 0.00 0.00 4.57
2127 2787 0.984230 TTTGAGACGGAGGGAGCAAT 59.016 50.000 0.00 0.00 0.00 3.56
2200 2860 9.911788 ATGAATGAAGTTATAGGTGTTTCTCAT 57.088 29.630 0.00 0.00 0.00 2.90
2236 3099 8.811017 TGGTTCAAAAGGAATGCATCTTTAATA 58.189 29.630 12.36 1.47 37.93 0.98
2241 3104 5.484715 CATGGTTCAAAAGGAATGCATCTT 58.515 37.500 0.00 0.00 37.93 2.40
2242 3105 4.622220 GCATGGTTCAAAAGGAATGCATCT 60.622 41.667 0.00 0.00 38.38 2.90
2246 3109 3.323751 AGCATGGTTCAAAAGGAATGC 57.676 42.857 0.00 0.00 38.64 3.56
2278 3141 7.440523 AATTCTTAGCTGTAGGAGTTGTTTG 57.559 36.000 0.00 0.00 0.00 2.93
2298 3161 8.225603 TGCCTCCAAGAGATTTATTGTAATTC 57.774 34.615 0.00 0.00 0.00 2.17
2314 3178 1.826385 ACGGAAAAGATGCCTCCAAG 58.174 50.000 0.00 0.00 0.00 3.61
2328 3192 4.274602 TGCAAAGGTTGATACTACGGAA 57.725 40.909 0.00 0.00 0.00 4.30
2334 3198 6.899393 TTTCATCTTGCAAAGGTTGATACT 57.101 33.333 0.00 0.00 46.24 2.12
2343 3207 6.971527 TTGGCAATATTTCATCTTGCAAAG 57.028 33.333 0.00 0.00 45.44 2.77
2354 3218 7.945033 TTTGTTGAAGTCTTGGCAATATTTC 57.055 32.000 12.10 12.10 0.00 2.17
2359 3223 6.294731 GGTCTATTTGTTGAAGTCTTGGCAAT 60.295 38.462 0.00 0.00 0.00 3.56
2372 3236 4.088648 GTCGAATTGCGGTCTATTTGTTG 58.911 43.478 0.00 0.00 41.33 3.33
2385 3249 0.924090 CGCTACTCCAGTCGAATTGC 59.076 55.000 0.00 0.00 0.00 3.56
2388 3252 3.251245 CAGTATCGCTACTCCAGTCGAAT 59.749 47.826 0.00 0.00 35.99 3.34
2391 3255 1.334239 GCAGTATCGCTACTCCAGTCG 60.334 57.143 0.00 0.00 35.99 4.18
2397 3261 1.397441 CGAGTCGCAGTATCGCTACTC 60.397 57.143 0.00 7.34 46.07 2.59



Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.